Figure 3: T cell lineage identity is encoded by both lineage-restricted and shared gene programs
Ziang Zhang
Last updated: 2026-09-10
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immgenT-GP-analysis/analysis/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | 60125af | Ziang Zhang | 2026-09-10 | Build site: Figure 4b on the shared column colours |
| html | 88ee847 | Ziang Zhang | 2026-09-10 | Build site: Figure 4b without the miniverse clusters |
| html | 5874416 | Ziang Zhang | 2026-09-10 | Build site: main Figure 4 inserted, Extended Data back to 1-7 |
| html | a7a481f | Ziang Zhang | 2026-09-09 | Build site: the rebuilt Figure 1d and the Extended Data renumbering |
| html | 1e88d7e | Ziang Zhang | 2026-09-04 | Build site: published captions and titles across all 24 pages |
| Rmd | 0267e5b | Ziang Zhang | 2026-09-04 | Captions from the published manuscript; trim editor notes off the page code |
| html | 19c977f | Ziang Zhang | 2026-09-02 | Build site: Extended Data 5-7 renumbered, Figure S5 page rebuilt |
| html | ae03072 | Ziang Zhang | 2026-08-19 | Build site: six pages rebuilt after the prose cleanup |
| html | 074dca1 | Ziang Zhang | 2026-08-05 | Build site: Extended Data tables reordered to six, internal notes off the pages |
| html | eeca07b | Ziang Zhang | 2026-08-05 | Keep pre-refactor provenance in panel comments off the published pages |
| html | cbcec52 | Ziang Zhang | 2026-07-30 | Build site: Extended Data Figure naming |
| html | ac650a0 | Ziang Zhang | 2026-07-30 | Build site: Figure S5 (ex-S6a) and Figure S6 as a-f |
| html | ae21d37 | Ziang Zhang | 2026-07-28 | Build site: republish after the reorder commits |
| html | d538aa2 | Ziang Zhang | 2026-07-28 | Build site: reordered Figures 6 / S6 / S3 and the new Figure 7b page |
| html | 029b0ae | Ziang Zhang | 2026-07-28 | Build site. |
| Rmd | 0f5b5da | Ziang Zhang | 2026-07-28 | Align all figure captions with captions_20260728_final.docx |
| html | 3fc3789 | Ziang Zhang | 2026-07-27 | Republish all 24 pages |
| Rmd | d04f8b8 | Ziang Zhang | 2026-07-27 | Figure 3: letter the J-L loading panels GP3 = J, GP29 = K, GP22 = L |
| html | 1390a03 | Ziang Zhang | 2026-07-27 | Republish all 24 pages |
| html | a4fc6a7 | Ziang Zhang | 2026-07-27 | Build site: 3M with Ctsw pinned |
| Rmd | 3fae8f8 | Ziang Zhang | 2026-07-27 | 3M: pin Ctsw to the top rows alongside Fcer1g/Ccl5/Cd7 |
| html | 7ba1d40 | Ziang Zhang | 2026-07-27 | Build site: 3M ranked by max(score) |
| Rmd | ed623c5 | Ziang Zhang | 2026-07-27 | 3M: rank the top 30 by max(score), making it a real "up-regulated genes" panel |
| html | adaef21 | Ziang Zhang | 2026-07-27 | Build site: panel fixes and PDF-derived assets |
| html | 5b19858 | Ziang Zhang | 2026-07-27 | Build site. |
| Rmd | 91ee059 | Ziang Zhang | 2026-07-26 | Select each panel’s code block by name, not by line number |
| html | 91ee059 | Ziang Zhang | 2026-07-26 | Select each panel’s code block by name, not by line number |
| Rmd | 620afca | Ziang Zhang | 2026-07-24 | Align Fig3/4/5 section titles with current numbers; reletter Fig4 to a-e |
| html | 620afca | Ziang Zhang | 2026-07-24 | Align Fig3/4/5 section titles with current numbers; reletter Fig4 to a-e |
| Rmd | 2873ad2 | Ziang Zhang | 2026-07-16 | Unify Fig 3/4/5 panel filenames with new figure numbers |
| html | 2873ad2 | Ziang Zhang | 2026-07-16 | Unify Fig 3/4/5 panel filenames with new figure numbers |
| Rmd | b197499 | Ziang Zhang | 2026-07-16 | Restructure main figures (renumber + split Figure 1) |
| html | b197499 | Ziang Zhang | 2026-07-16 | Restructure main figures (renumber + split Figure 1) |
| html | 92021bf | Ziang Zhang | 2026-07-02 | Build site. |
| html | 827c89b | Ziang Zhang | 2026-07-02 | Build site. |
| Rmd | 8ac7f9f | Ziang Zhang | 2026-07-02 | Add data provenance notes to each script; remove conversational |
| Rmd | f9db962 | Ziang Zhang | 2026-07-02 | Simplify layout: drop old code/script folders, rename |
| html | c6e5086 | Ziang Zhang | 2026-07-02 | Build site. |
| html | 5a79883 | Ziang Zhang | 2026-07-02 | Build site. |
| Rmd | 2b0e445 | Ziang Zhang | 2026-07-02 | Fix GitHub source links to point at the new |
| html | cf1d0ac | Ziang Zhang | 2026-07-02 | Build site. |
| Rmd | 06b2461 | Ziang Zhang | 2026-07-02 | Initial commit: immgenT-GP-analysis |
| html | 06b2461 | Ziang Zhang | 2026-07-02 | Initial commit: immgenT-GP-analysis |
All panels are produced by script/Figure3.R.
The code below is shown for reference (not re-executed on this page);
the images are its pre-rendered output.
Setup
Data loading, shared across all panels below.
# Figure 3. GPs and lineages.
#
# Panels produced:
# 3A Swarm plot of per-GP AUC (predicting major lineage), up-regulated
# GPs only, with GP3/22/29 force-highlighted.
# 3B Structure plot of 6 lineage-defining GPs across major lineages.
# 3C,3E,3G GP loading on the global MDE, for GP68, GP30, GP58.
# 3D,3F,3H Per-gene view (score vs. mean expression) for GP68, GP30, GP58.
# 3I MDE restricted to gdT/CD8aa/DN, colored by lineage.
# 3J,3K,3L GP loading on the gdT/CD8aa/DN MDE, for GP3, GP29, GP22.
# 3M Heatmap of the top-30 up-regulated gene scores for GP3, GP29, GP22.
#
# Required inputs (data/) -- see code/README.md's "Data provenance" table
# for the full picture:
# igt1_96_..._ADTonly.Rds [primary input Seurat object]
# L_pm_filtered.rds, F_pm_filtered.rds [code/pipeline/01b_filter_cells.R]
# umap_result.rds [gap, no producer script here]
# level_1_AUC_list_figure_no_thymocytes_healthy.rds [code/pipeline/02_compute_auc.R]
# mean_shifted_log_expr.rds [gap, no producer script here]
library(ggplot2)
library(ggrepel)
library(dplyr)
library(tidyr)
library(tibble)
library(scattermore)
library(pheatmap)
library(fastTopics) # structure_plot()
data_path <- "data/"
figure_path <- "figures/final-selected/Figure 3/"
source("code/R/plot_utils.R") # lineage_colors()
source("code/R/lineage_plots.R") # plot_gp_swarm(), plot_loadings_on_mde()
source("code/R/volcano_helpers.R") # plot_gp_signature_volcano(), normalize_maxabs()
source("code/R/cross_gp_helpers.R") # plot_cross_gp_heatmap()
# ============================================================
# Load data
# ============================================================
seurat_meta <- readRDS(paste0(
data_path,
"igt1_96_withtotalvi20260206_clean_ADTonly.Rds"
))@meta.data
L_pm_filtered <- readRDS(paste0(data_path, "L_pm_filtered.rds"))
seurat_meta_filtered <- seurat_meta[rownames(L_pm_filtered), ]
mde_result <- readRDS(paste0(data_path, "umap_result.rds"))
colnames(mde_result) <- c("MDE_1", "MDE_2")
mde_result <- mde_result[rownames(L_pm_filtered), ]
df_mde <- as.data.frame(mde_result)
level_1_AUC_list <- readRDS(paste0(data_path, "level_1_AUC_list_figure_no_thymocytes_healthy.rds"))
# Rename K## to GP## for display consistency
colnames(L_pm_filtered) <- gsub("^K", "GP", colnames(L_pm_filtered))
colnames(level_1_AUC_list$auc) <- gsub(
"^K",
"GP",
colnames(level_1_AUC_list$auc)
)(a) AUC swarm plot by lineage
# ============================================================
# 3A: AUC swarm, up-regulated GPs only, GP3/22/29 forced highlight
# ============================================================
selected_lineage_in_order <- c("CD8", "CD4", "Treg", "gdT", "CD8aa", "Tz", "DN")
level_1_categories <- as.character(unique(
seurat_meta_filtered$annotation_level1
))
mean_loading_matrix <- t(sapply(level_1_categories, function(cat) {
cells_in_cat <- which(seurat_meta_filtered$annotation_level1 == cat)
colMeans(L_pm_filtered[cells_in_cat, , drop = FALSE], na.rm = TRUE)
}))
mean_loading_matrix_selected <- mean_loading_matrix[selected_lineage_in_order, ]
non_thymocyte_cells <- which(
seurat_meta_filtered$annotation_level1 != "thymocyte"
)
mean_loading_vec <- colMeans(
L_pm_filtered[non_thymocyte_cells, , drop = FALSE],
na.rm = TRUE
)
AUC_mat_selected <- level_1_AUC_list$auc[selected_lineage_in_order, ]
p_3A <- plot_gp_swarm(
AUC_mat_selected,
loading_mat = mean_loading_matrix,
overall_loading_vec = mean_loading_vec,
filter_positive = TRUE,
forced_highlights = list(
gdT = c("GP22", "GP29", "GP3"),
CD8aa = c("GP22", "GP29", "GP3"),
DN = c("GP22", "GP29", "GP3")
),
top_k_labels = 1,
threshold_line = 0.5,
title = "Up-regulated GP Predictive Performance (AUC)",
subtitle = "Up-regulated GPs (Loading >= Overall Mean); triangles mark forced highlights that are down-regulated",
y_label = "Area Under the Curve (AUC)",
italic_subtitle = TRUE
)
ggsave(
filename = paste0(figure_path, "3A.pdf"),
plot = p_3A,
width = 10,
height = 6
)
Fig. 3a. Swarm plot showing the AUC of each GP for predicting major T cell lineage. The top GPs for each lineage are highlighted.
(b) Structure plot of lineage-defining GPs
# ============================================================
# 3B: Structure plot of 6 lineage-defining GPs
# ============================================================
set.seed(1234)
color_coding <- ZemmourLib::immgent_colors$level1
level1_category_to_factor <- c(
"Treg" = "GP68",
"CD8" = "GP58",
"Tz" = "GP30",
"DN" = "GP22",
"CD8aa" = "GP29",
"gdT" = "GP3"
)
fit2 <- L_pm_filtered[, level1_category_to_factor, drop = FALSE]
cell_type <- seurat_meta[rownames(fit2), "annotation_level1"]
cells <- which(cell_type == "CD4" | cell_type == "CD8")
cells <- sample(cells, 1e5)
cells <- sort(c(
cells,
which(
cell_type != "CD4" &
cell_type != "CD8" &
cell_type != "thymocyte" &
cell_type != "DP"
)
))
p_3B <- structure_plot(
fit2[cells, ],
gap = 40,
n = 10000,
colors = color_coding[names(level1_category_to_factor)],
grouping = cell_type[cells]
) +
labs(y = "membership", color = "", fill = "") +
guides(fill = guide_legend(nrow = 1), color = guide_legend(nrow = 1)) +
theme(
legend.position = "bottom",
legend.direction = "horizontal",
legend.box = "horizontal",
axis.text.x = element_text(size = 10, angle = 45, hjust = 1),
axis.text.y = element_text(size = 12),
axis.title = element_text(size = 14, face = "bold"),
legend.text = element_text(size = 12),
legend.title = element_text(size = 13)
)
ggsave(
filename = paste0(figure_path, "3B.pdf"),
plot = p_3B,
width = 10,
height = 6,
dpi = 300
)
Fig. 3b. Structure plot showing single-cell activity of the lineage-related GPs identified in (a), grouped by lineage.
(c) GP68 activity on the all-T MDE
# ============================================================
# 3C/3E/3G: GP68, GP30, GP58 loading on the global MDE (reconstructed)
# ============================================================
p_3C <- plot_loadings_on_mde(
mde = df_mde,
loading = L_pm_filtered[rownames(df_mde), "GP68"],
factor_num = 68,
size = 0.6,
bg_alpha = 0.1,
bg_color = "grey90"
)
ggsave(
filename = paste0(figure_path, "3C.pdf"),
plot = p_3C,
width = 5,
height = 4
)
Fig. 3c. All-T MDE colored by GP68 activity.
(d) GP68 signature volcano
# ============================================================
# 3D/3F/3H: "signature volcano" per-gene view for GP68, GP30, GP58.
# ============================================================
F_pm_filtered_3d <- readRDS(paste0(data_path, "F_pm_filtered.rds"))
colnames(F_pm_filtered_3d) <- paste0("GP", seq_len(ncol(F_pm_filtered_3d)))
F_pm_normalized_3d <- normalize_maxabs(F_pm_filtered_3d)
mean_shifted_log_expr <- readRDS(paste0(data_path, "mean_shifted_log_expr.rds"))
p_3D <- plot_gp_signature_volcano(
"GP68",
F_pm_normalized_3d,
mean_shifted_log_expr,
threshold = 0.1,
n_label = 100,
bg_alpha = 0.2
)
ggsave(
filename = paste0(figure_path, "3D.pdf"),
plot = p_3D,
width = 7,
height = 5.5
)
Fig. 3d. Gene scores for GP68. The x-axis shows the GP68 gene score, and the y-axis shows mean expression across all T cells (log-transformed).
(e) GP30 activity on the all-T MDE
p_3E <- plot_loadings_on_mde(
mde = df_mde,
loading = L_pm_filtered[rownames(df_mde), "GP30"],
factor_num = 30,
size = 0.6,
bg_alpha = 0.1,
bg_color = "grey90"
)
ggsave(
filename = paste0(figure_path, "3E.pdf"),
plot = p_3E,
width = 5,
height = 4
)
Fig. 3e. All-T MDE colored by GP30 activity.
(f) GP30 signature volcano
p_3F <- plot_gp_signature_volcano(
"GP30",
F_pm_normalized_3d,
mean_shifted_log_expr,
threshold = 0.1,
n_label = 100,
bg_alpha = 0.2
)
ggsave(
filename = paste0(figure_path, "3F.pdf"),
plot = p_3F,
width = 7,
height = 5.5
)
Fig. 3f. Gene scores for GP30, shown as in (d).
(g) GP58 activity on the all-T MDE
p_3G <- plot_loadings_on_mde(
mde = df_mde,
loading = L_pm_filtered[rownames(df_mde), "GP58"],
factor_num = 58,
size = 0.6,
bg_alpha = 0.1,
bg_color = "grey90"
)
ggsave(
filename = paste0(figure_path, "3G.pdf"),
plot = p_3G,
width = 5,
height = 4
)
Fig. 3g. All-T MDE colored by GP58 activity.
(h) GP58 signature volcano
p_3H <- plot_gp_signature_volcano(
"GP58",
F_pm_normalized_3d,
mean_shifted_log_expr,
threshold = 0.1,
n_label = 83,
bg_alpha = 0.2
)
ggsave(
filename = paste0(figure_path, "3H.pdf"),
plot = p_3H,
width = 7,
height = 5.5
)
Fig. 3h. Gene scores for GP58, shown as in (d).
(i) gdT/CD8aa/DN MDE by lineage
# ============================================================
# 3I: MDE restricted to gdT/CD8aa/DN, colored by lineage
# (excludes proliferating / miniverse subsets)
# ============================================================
gcd_lineages <- c("gdT", "CD8aa", "DN")
gcd_cells <- seurat_meta_filtered$cellID[
seurat_meta_filtered$annotation_level1 %in%
gcd_lineages &
!(seurat_meta_filtered$annotation_level2_group %in%
c("proliferating", "miniverse"))
]
df_mde_gcd <- df_mde[gcd_cells, ]
df_mde_gcd$annotation_level1 <- factor(
seurat_meta_filtered[gcd_cells, "annotation_level1"],
levels = gcd_lineages
)
p_3I <- ggplot(df_mde_gcd, aes(x = MDE_1, y = MDE_2)) +
scattermore::geom_scattermore(
aes(color = annotation_level1),
pointsize = 1.2
) +
scale_color_manual(values = lineage_colors()[gcd_lineages]) +
coord_equal() +
theme_classic() +
labs(
title = "MDE: gdT / CD8aa / DN",
x = "MDE 1",
y = "MDE 2",
color = "Cell Type"
) +
theme(
legend.text = element_text(size = 10),
legend.key.size = unit(1.5, "lines")
) +
guides(color = guide_legend(override.aes = list(size = 4)))
ggsave(
filename = paste0(figure_path, "3I.pdf"),
plot = p_3I,
width = 5,
height = 5
)
Fig. 3i. All-T MDE subsetted to show only gdT cells, CD8aa T cells, and DN T cells. Cells are colored by (i) lineage (gdT in green, CD8aa in purple, and DN in blue).
(j-l) GP3, GP29, GP22 loading on the gdT/CD8aa/DN MDE
# ============================================================
# 3J/3K/3L: GP3, GP29, GP22 loading on the gdT/CD8aa/DN MDE
# ============================================================
# Panel lettering is GP3 = J, GP29 = K, GP22 = L, matching the GP3/GP29/GP22
# column order of 3M so the figure reads left-to-right in one order throughout.
gp_letter <- c("GP3" = "3J", "GP29" = "3K", "GP22" = "3L")
for (gp_name in names(gp_letter)) {
gp_num <- as.numeric(sub("^GP", "", gp_name))
p_loading <- plot_loadings_on_mde(
mde = df_mde_gcd[, c("MDE_1", "MDE_2")],
loading = L_pm_filtered[gcd_cells, gp_name],
factor_num = gp_num,
size = 0.6,
bg_alpha = 0.1,
bg_color = "grey90"
)
ggsave(
filename = paste0(figure_path, gp_letter[gp_name], ".pdf"),
plot = p_loading,
width = 5,
height = 4
)
}
Fig. 3j-l. The same subsetted MDE as in (i), with cells colored by (j) GP3 activity, (k) GP29 activity, and (l) GP22 activity.
(m) Top-30 gene score heatmap for GP3/GP29/GP22
# ============================================================
# 3M: cross-GP heatmap, top-30 UP-REGULATED gene weights for GP3, GP29, GP22
# (heatmap built by code/R/cross_gp_helpers.R)
#
# Three choices define the panel:
# - rank_by = "pos": top 30 by max(score), i.e. genuinely up-regulated
# (see the note at the call below)
# - column order GP3, GP29, GP22
# - Fcer1g/Ccl5/Cd7/Ctsw pinned to the top 4 rows via `pin_top`
# ============================================================
F_pm_filtered_3m <- readRDS(paste0(data_path, "F_pm_filtered.rds"))
colnames(F_pm_filtered_3m) <- paste0("GP", seq_len(ncol(F_pm_filtered_3m)))
F_pm_norm_3m <- normalize_maxabs(F_pm_filtered_3m)
common_genes_3m <- intersect(rownames(F_pm_norm_3m), names(mean_shifted_log_expr))
gps_3m <- c("GP3", "GP29", "GP22")
mat_3m <- F_pm_norm_3m[common_genes_3m, gps_3m, drop = FALSE]
p_3M <- plot_cross_gp_heatmap(
mat_3m, gps_3m,
# rank_by = "pos": candidates are the genes positive in at least one of the
# three GPs (direction = "pos"), ranked by max(score) across them.
feat_label = "Gene", n_genes = 30, direction = "pos", rank_by = "pos",
threshold = 0.05, colorscheme = "bwr", cluster_r = TRUE, cluster_c = FALSE,
pin_top = c("Fcer1g", "Ccl5", "Cd7", "Ctsw")
)
ph_3m <- max(4, 2 + 30 * 0.14)
pw_3m <- max(5, 3 + length(gps_3m) * 0.8)
ggsave(filename = paste0(figure_path, "3M.pdf"), plot = p_3M, width = pw_3m, height = ph_3m)
Fig. 3m. Heatmap showing the top 30 genes upregulated in GP3, GP22, and GP29.
sessionInfo()R version 4.5.1 (2025-06-13)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.6.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1
locale:
[1] en_CA/en_CA/en_CA/C/en_CA/en_CA
time zone: America/Chicago
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] vctrs_0.7.3 cli_3.6.6 knitr_1.50 rlang_1.2.0
[5] xfun_0.55 stringi_1.8.9 otel_0.2.0 promises_1.5.0
[9] jsonlite_2.0.0 workflowr_1.7.2 glue_1.8.1 rprojroot_2.1.1
[13] git2r_0.36.2 htmltools_0.5.9 httpuv_1.6.16 sass_0.4.10
[17] rmarkdown_2.30 evaluate_1.0.5 jquerylib_0.1.4 tibble_3.3.0
[21] fastmap_1.2.0 yaml_2.3.12 lifecycle_1.0.5 whisker_0.4.1
[25] stringr_1.6.0 compiler_4.5.1 fs_1.6.6 Rcpp_1.1.1-1.1
[29] pkgconfig_2.0.3 later_1.4.4 digest_0.6.39 R6_2.6.1
[33] pillar_1.11.1 magrittr_2.0.5 bslib_0.9.0 tools_4.5.1
[37] cachem_1.1.0